Config

Job: expected-2

align:
  mafft:
  - --6merpair
  - --keeplength
  - --addfragments
  resources:
    mem_mb: 8000
    runtime: 10
  threads: 4
all:
  threads_max: 64
  update_default_resources: null
beast:
  beast:
  - -beagle_SSE
  - -seed 98202873
  dynamic:
  - ePopSize=0.3
  - Date.dateFormat=yyyy/MM/dd
  - Date.delimiter=_
  - mutationRate=1.0
  - mcmc.chainLength=10000
  - treelog.logEvery=1000
  - tracelog.logEvery=1000
  resources:
    mem_mb: 16000
    runtimtime: 1200
  threads: 6
data:
- /Users/smutch/work/mdap/collabs/2022/duchene/mccoy/tests/expected/runs/run_1/data/combined/expected-1.fasta
- /Users/smutch/work/mdap/collabs/2022/duchene/mccoy/tests/data2.fasta
id: expected-2
inherit: tests/expected/runs/run_1
project_id: expected
project_path: /Users/smutch/work/mdap/collabs/2022/duchene/mccoy/tests/expected
run_id: 2
run_name: run_2
tree:
  iqtree2:
  - -nt AUTO
  - -m HKY+G
  - -bb 1000
  - -seed 847202098
  resources:
    mem_mb: 16000
    runtime: 20
  threads: 10

Alignment

General Characteristics
=======================
138	Number of taxa
1734	Alignment length
81	Parsimony informative sites
190	Variable sites
1544	Constant sites

Character Frequencies
=====================
Y	1
W	1
T	57893
R	1
M	2
G	52082
C	47452
A	81527
-	333
GC content: 0.4165
Relative composition variability: 0.0035

Pairwise Identity

The proportion of colums that agree between pairs in the alignment. See PhyKIT docs.

mean: 0.9926
median: 0.9925
25th percentile: 0.9908
75th percentile: 0.9948
minimum: 0.9804
maximum: 1.0
standard deviation: 0.0031
variance: 0.0

Maximum Likelihood Tree

Quality Control

Beast

Bibliography